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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs1490730395

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:50952182 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000034 (9/264690, TOPMED)
G=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HIGD1C : Intron Variant
SLC11A2 : 500B Downstream Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14050 A=1.00000 G=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 A=1.000 G=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 A=1.000 G=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 A=1.000 G=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 A=1.000 G=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Sub 496 A=1.000 G=0.000 1.0 0.0 0.0 N/A


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 A=0.999966 G=0.000034
Allele Frequency Aggregator Total Global 14050 A=1.00000 G=0.00000
Allele Frequency Aggregator European Sub 9690 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2898 A=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 G=0.000
Allele Frequency Aggregator Other Sub 496 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 12 NC_000012.12:g.50952182A>G
GRCh37.p13 chr 12 NC_000012.11:g.51345965A>G
Gene: HIGD1C, HIG1 hypoxia inducible domain family member 1C (plus strand)
Molecule type Change Amino acid[Codon] SO Term
HIGD1C transcript NM_001109619.4:c. N/A Genic Upstream Transcript Variant
HIGD1C transcript variant X1 XM_017019783.3:c.6-259A>G N/A Intron Variant
HIGD1C transcript variant X2 XM_017019784.3:c.6-259A>G N/A Intron Variant
HIGD1C transcript variant X4 XM_011538649.3:c. N/A Genic Upstream Transcript Variant
HIGD1C transcript variant X3 XM_017019785.2:c. N/A Genic Upstream Transcript Variant
Gene: SLC11A2, solute carrier family 11 member 2 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
SLC11A2 transcript variant 4 NM_000617.3:c. N/A N/A
SLC11A2 transcript variant 1 NM_001174125.2:c. N/A N/A
SLC11A2 transcript variant 2 NM_001174126.2:c. N/A N/A
SLC11A2 transcript variant 3 NM_001174127.2:c. N/A N/A
SLC11A2 transcript variant 5 NM_001174128.2:c. N/A N/A
SLC11A2 transcript variant 6 NM_001174129.1:c. N/A N/A
SLC11A2 transcript variant 7 NM_001174130.2:c. N/A N/A
SLC11A2 transcript variant 10 NM_001379446.1:c. N/A N/A
SLC11A2 transcript variant 11 NM_001379447.1:c. N/A N/A
SLC11A2 transcript variant 12 NM_001379448.1:c. N/A N/A
SLC11A2 transcript variant 16 NM_001379455.1:c. N/A N/A
SLC11A2 transcript variant 8 NR_033421.2:n. N/A N/A
SLC11A2 transcript variant 9 NR_033422.2:n. N/A N/A
SLC11A2 transcript variant 13 NR_166668.1:n. N/A N/A
SLC11A2 transcript variant 14 NR_166669.1:n. N/A N/A
SLC11A2 transcript variant 15 NR_166670.1:n. N/A N/A
SLC11A2 transcript variant X8 XM_011538404.4:c. N/A N/A
SLC11A2 transcript variant X5 XM_011538405.4:c. N/A N/A
SLC11A2 transcript variant X4 XM_047428887.1:c. N/A N/A
SLC11A2 transcript variant X2 XR_001748720.2:n. N/A Downstream Transcript Variant
SLC11A2 transcript variant X6 XR_007063077.1:n. N/A Downstream Transcript Variant
SLC11A2 transcript variant X7 XR_007063078.1:n. N/A Downstream Transcript Variant
SLC11A2 transcript variant X9 XR_007063079.1:n. N/A N/A
SLC11A2 transcript variant X1 XR_429104.2:n. N/A N/A
SLC11A2 transcript variant X3 XR_944555.2:n. N/A N/A
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement A= G
GRCh38.p14 chr 12 NC_000012.12:g.50952182= NC_000012.12:g.50952182A>G
GRCh37.p13 chr 12 NC_000012.11:g.51345965= NC_000012.11:g.51345965A>G
HIGD1C transcript variant X1 XM_017019783.3:c.6-259= XM_017019783.3:c.6-259A>G
HIGD1C transcript variant X2 XM_017019784.3:c.6-259= XM_017019784.3:c.6-259A>G
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 TOPMED ss4918124454 Apr 25, 2021 (155)
2 TopMed NC_000012.12 - 50952182 Apr 25, 2021 (155)
3 ALFA NC_000012.12 - 50952182 Apr 25, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
133670111, 3202706990, ss4918124454 NC_000012.12:50952181:A:G NC_000012.12:50952181:A:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1490730395

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top▲ Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post820+afb47a3d